I may be missing something, but I am perplexed by the suggestion of having your body calibrated to the lens. If you have several lenses which are off at varying +/- values, then should we have a dedicated body for each lens?
I assume you're referring to the OP's statement about 'factory calibration of body to lens.' That's not really what Canon Service does. Rather, if you send in a body they adjust it to match a 'reference' lens (presumably one dead center in the tolerance range), and if you send in a lens they adjust it to a 'reference' body of the type you have. If you send body and lens, they adjust both to the reference counterpart, not to each other.
That's right. If you send the pair to Canon for calibration then they calibrate for just that pair, and if you have other lenses then they will be correctly matched only if they have the same focus as the calibrated lens. But, if you calibrate the the AFMA yourself, then you can do it for all your individual lenses.
A key difference is that Canon can make more complex adjustments to a lens than AFMA. For example, they can adjust a zoom lens at several focal lengths, not just one for the whole zoom range (or the ends with interpolation on recent bodies) as we do with AFMA.